app-3Dfreesurfs

This application will create a 3D surface for 87 freesurfer labels from the aparc+aseg.mgz file.

Author

• Lindsey Kitchell (kitchell@indiana.edu)

Contributors

• Steven O'Reilly (stevengeeky@gmail.com)

Funding

Citations

We kindly ask that you cite the following when publishing papers and code using this code.

1. Avesani, P., McPherson, B., Hayashi, S. et al. The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Sci Data 6, 69 (2019). https://doi.org/10.1038/s41597-019-0073-y

Running the App

On Brainlife.io

You can submit this App online at https://brainlife.io/app/5aa826baf315ba00317fe086# via the "Execute" tab.

Running Locally (on your machine)

1. git clone this repo.
2. Inside the cloned directory, create config.json with something like the following content with paths to your input files.

{
    "filetype": "vtk",
    "freesurfer": "../5b96d2cb161e01002a320742/5967bffa9b45c212bbec8958/output"
}

If you have singlarity install on your local machine:

3. Launch the App by executing main

./main

Otherwise:

3. execute convertfiles.sh and then main.py in python.

Sample Datasets

If you don't have your own input file, you can download sample datasets from Brainlife.io, or you can use Brainlife CLI.

Output

The output of this app will be a folder with a surface mesh file for each of the 87 freesrufer labels.

Dependencies

This App only requires singularity to run. If you don't have singularity, you will need to install following dependencies.

• Freesurfer: https://surfer.nmr.mgh.harvard.edu/
• VTK: https://www.vtk.org/download/ (easiest to just use Anaconda (https://www.anaconda.com/) which comes with vtk)